title: Sorbitol RPL16a-ZZ total vs reference (2)

description:
Simple annotation: RNA coimmunoprecipitation, Condition media
Image: http://smd.stanford.edu/MicroArray/gifs/2006-09/70011.gif
Measurement: time(absolute) 10 m
Growth Condition: Sorbitol

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 680, 19800; Software: type: feature extraction; Performer: Regula,,Halbeisen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-08-29; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 390; Parameter Laser on time = 14381; Parameter Laser Power = 2.98; Parameter Scan Time = 14:32:52; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 24.94; Performer: Regula,,Halbeisen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-08-29; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 340; Parameter Scan Power = 100; Parameter Laser on time = 14380; Parameter Laser Power = 3.63; Parameter Scan Time = 14:32:52; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 24.94; Performer: Regula,,Halbeisen


title: Menadione RPL16a-ZZ IP poly vs reference (4)

status: Public on May 12 2009

type: RNA

city: ETH Hoenggerberg, Zuerich

first: Andre

last: Gerber

address: Wolfgang Pauli Str. 10, HCI H396

department: Institute of Pharmaceutical Science

country: Switzerland

institute: Swiss Federal Institute of Technology

description:
Simple annotation: RNA coimmunoprecipitation, Condition media
Image: http://smd.stanford.edu/MicroArray/gifs/2006-10/70641.gif
Measurement: time(absolute) 20 m
Growth Condition: Menadione

hyb_protocol: not provided

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1600, 19960; Software: type: feature extraction; Performer: Regula,,Halbeisen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-10-06; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 390; Parameter Laser on time = 15276; Parameter Laser Power = 2.93; Parameter Scan Time = 11:59:45; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 24.38; Performer: Regula,,Halbeisen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-10-06; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 330; Parameter Scan Power = 100; Parameter Laser on time = 15276; Parameter Laser Power = 3.61; Parameter Scan Time = 11:59:45; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 24.38; Performer: Regula,,Halbeisen

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: Reference RNA

label_protocol: not provided

extract_protocol: not provided

tag: Reference RNA

source_name: IP RNA RPL16a-ZZ

tag: IP RNA RPL16a-ZZ


title: Menadione RPL16a-ZZ total vs reference (1)

description:
Simple annotation: RNA coimmunoprecipitation, Condition media
Image: http://smd.stanford.edu/MicroArray/gifs/2006-09/70010.gif
Measurement: time(absolute) 20 m
Growth Condition: Menadione

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 720, 19840; Software: type: feature extraction; Performer: Regula,,Halbeisen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-08-29; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 400; Parameter Laser on time = 14366; Parameter Laser Power = 2.98; Parameter Scan Time = 14:18:51; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 25.00; Performer: Regula,,Halbeisen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-08-29; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 340; Parameter Scan Power = 100; Parameter Laser on time = 14366; Parameter Laser Power = 3.61; Parameter Scan Time = 14:18:51; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 25.00; Performer: Regula,,Halbeisen

source_name: Total RNA RPL16a-ZZ

tag: Total RNA RPL16a-ZZ


title: Sorbitol RPL16a-ZZ total vs reference (1)

description:
Simple annotation: RNA coimmunoprecipitation, Condition media
Image: http://smd.stanford.edu/MicroArray/gifs/2006-08/69612.gif
Measurement: time(absolute) 10 m
Growth Condition: Sorbitol

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 760, 20000; Software: type: feature extraction; Performer: Regula,,Halbeisen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-08-08; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 390; Parameter Laser on time = 13663; Parameter Laser Power = 2.95; Parameter Scan Time = 10:34:37; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 25.25; Performer: Regula,,Halbeisen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-08-08; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 350; Parameter Scan Power = 100; Parameter Laser on time = 13663; Parameter Laser Power = 3.60; Parameter Scan Time = 10:34:37; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 25.25; Performer: Regula,,Halbeisen


title: CFW RPL16a-ZZ total vs reference (2)

description:
Simple annotation: RNA coimmunoprecipitation, Condition media
Image: http://smd.stanford.edu/MicroArray/gifs/2006-02/67014.gif
Measurement: time(absolute) 20 m
Growth Condition: CFW

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1000, 19160; Software: type: feature extraction; Performer: Regula,,Halbeisen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-02-10; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 480; Parameter Laser on time = 9382; Parameter Laser Power = 3.08; Parameter Scan Time = 11:42:58; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 24.06; Performer: Regula,,Halbeisen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-02-10; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 380; Parameter Scan Power = 100; Parameter Laser on time = 9382; Parameter Laser Power = 3.59; Parameter Scan Time = 11:42:58; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 24.06; Performer: Regula,,Halbeisen

source_name: total RNA RPL16a-ZZ

tag: total RNA RPL16a-ZZ


title: Menadione RPL16a-ZZ total vs reference (4)

description:
Simple annotation: RNA coimmunoprecipitation, Condition media
Image: http://smd.stanford.edu/MicroArray/gifs/2006-10/70639.gif
Measurement: time(absolute) 20 m
Growth Condition: Menadione

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1720, 19840; Software: type: feature extraction; Performer: Regula,,Halbeisen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-10-06; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 380; Parameter Laser on time = 15250; Parameter Laser Power = 2.92; Parameter Scan Time = 11:33:24; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 24.00; Performer: Regula,,Halbeisen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-10-06; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 320; Parameter Scan Power = 100; Parameter Laser on time = 15250; Parameter Laser Power = 3.60; Parameter Scan Time = 11:33:24; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 24.00; Performer: Regula,,Halbeisen

source_name: Total RNA RPl16a-ZZ

tag: Total RNA RPl16a-ZZ


title: CFW RPL16a-ZZ IP poly vs reference (1)

description:
Simple annotation: RNA coimmunoprecipitation, Condition media
Image: http://smd.stanford.edu/MicroArray/gifs/2006-01/66392.gif
Measurement: time(absolute) 20 m
Growth Condition: CFW

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 920, 19200; Software: type: feature extraction; Performer: Regula,,Halbeisen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-01-06; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 410; Parameter Laser on time = 9261; Parameter Laser Power = 3.11; Parameter Scan Time = 10:31:25; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 23.38; Performer: Regula,,Halbeisen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-01-06; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 410; Parameter Scan Power = 100; Parameter Laser on time = 9261; Parameter Laser Power = 3.60; Parameter Scan Time = 10:31:25; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 23.38; Performer: Regula,,Halbeisen


title: CFW100 RPL16a-ZZ total vs reference (3)

description:
Simple annotation: RNA coimmunoprecipitation, Condition media
Image: http://smd.stanford.edu/MicroArray/gifs/2006-10/70712.gif
Measurement: time(absolute) 20 m
Growth Condition: CFW

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 2320, 19280; Software: type: feature extraction; Performer: Regula,,Halbeisen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-10-17; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 430; Parameter Laser on time = 15564; Parameter Laser Power = 2.94; Parameter Scan Time = 09:01:35; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 23.44; Performer: Regula,,Halbeisen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-10-17; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 340; Parameter Scan Power = 100; Parameter Laser on time = 15564; Parameter Laser Power = 3.60; Parameter Scan Time = 09:01:35; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 23.44; Performer: Regula,,Halbeisen


title: RPL16a-ZZ total vs reference (4)

description:
Simple annotation: RNA coimmunoprecipitation, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68675.gif
Measurement: time(absolute) 0 m
Growth Condition: none

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 920, 20120; Software: type: feature extraction; Performer: Regula,,Halbeisen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-05-26; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 410; Parameter Laser on time = 11823; Parameter Laser Power = 2.99; Parameter Scan Time = 09:56:41; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 24.38; Performer: Regula,,Halbeisen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-05-26; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 370; Parameter Scan Power = 100; Parameter Laser on time = 11822; Parameter Laser Power = 3.58; Parameter Scan Time = 09:56:41; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 24.38; Performer: Regula,,Halbeisen

source_name: RPL16a-ZZ total RNA

tag: RPL16a-ZZ total RNA


title: RPL16a-ZZ IP poly vs reference (4)

description:
Simple annotation: RNA coimmunoprecipitation, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68681.gif
Measurement: time(absolute) 0 m
Growth Condition: none

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 880, 20040; Software: type: feature extraction; Performer: Regula,,Halbeisen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-05-30; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 390; Parameter Laser on time = 11938; Parameter Laser Power = 3.05; Parameter Scan Time = 10:28:35; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 24.06; Performer: Regula,,Halbeisen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-05-30; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 360; Parameter Scan Power = 100; Parameter Laser on time = 11938; Parameter Laser Power = 3.58; Parameter Scan Time = 10:28:35; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 24.06; Performer: Regula,,Halbeisen


title: RPL16a-ZZ total vs reference (2)

description:
Simple annotation: RNA coimmunoprecipitation, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2006-02/67012.gif
Measurement: time(absolute) 0 m
Growth Condition: none

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1040, 19120; Software: type: feature extraction; Performer: Regula,,Halbeisen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-02-10; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 460; Parameter Laser on time = 9351; Parameter Laser Power = 3.15; Parameter Scan Time = 11:11:21; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 23.69; Performer: Regula,,Halbeisen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-02-10; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 370; Parameter Scan Power = 100; Parameter Laser on time = 9350; Parameter Laser Power = 3.57; Parameter Scan Time = 11:11:21; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 23.69; Performer: Regula,,Halbeisen


title: AAs starvation RPL16a-ZZ total vs reference (1)

description:
Simple annotation: RNA coimmunoprecipitation, AA_starvation
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/66121.gif
Measurement: time(absolute) 20 m
Growth Condition: Amino acid starvation

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1040, 19840; Software: type: feature extraction; Performer: Regula,,Halbeisen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-12-20; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 420; Parameter Laser on time = 9087; Parameter Laser Power = 3.15; Parameter Scan Time = 13:42:53; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 23.75; Performer: Regula,,Halbeisen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-12-20; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 460; Parameter Scan Power = 100; Parameter Laser on time = 9087; Parameter Laser Power = 3.61; Parameter Scan Time = 13:42:53; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 23.75; Performer: Regula,,Halbeisen


title: RPL16a-ZZ IP polybeads vs reference (5)

description:
Simple annotation: RNA coimmunoprecipitation, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2006-08/69657.gif
Measurement: time(absolute) 0 m
Growth Condition: none

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 880, 19880; Software: type: feature extraction; Performer: Regula,,Halbeisen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-08-09; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 370; Parameter Laser on time = 13935; Parameter Laser Power = 2.85; Parameter Scan Time = 11:46:07; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 25.75; Performer: Regula,,Halbeisen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-08-09; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 390; Parameter Scan Power = 100; Parameter Laser on time = 13934; Parameter Laser Power = 3.63; Parameter Scan Time = 11:46:07; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 25.75; Performer: Regula,,Halbeisen


title: Rpl16a-ZZ Gradient (3)

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2009-01/82650.gif
Media: SC

scan_protocol: GenePix 4200A

source_name: Total RNA Rpl16a-ZZ

tag: reference

value: Total RNA Rpl16a-ZZ

source_name: Gradient RNA Rpl16a-ZZ

tag: test

value: Gradient RNA Rpl16a-ZZ


title: Menadione RPL16a-ZZ IP poly vs reference (3)

description:
Simple annotation: RNA coimmunoprecipitation, Condition media
Image: http://smd.stanford.edu/MicroArray/gifs/2006-10/70640.gif
Measurement: time(absolute) 20 m
Growth Condition: Menadione

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1440, 19320; Software: type: feature extraction; Performer: Regula,,Halbeisen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-10-06; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 390; Parameter Laser on time = 15263; Parameter Laser Power = 2.92; Parameter Scan Time = 11:46:38; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 24.25; Performer: Regula,,Halbeisen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-10-06; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 340; Parameter Scan Power = 100; Parameter Laser on time = 15262; Parameter Laser Power = 3.61; Parameter Scan Time = 11:46:38; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 24.25; Performer: Regula,,Halbeisen


title: RPL16a-ZZ total vs reference (3)

description:
Simple annotation: RNA coimmunoprecipitation, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67969.gif
Measurement: time(absolute) 0 m
Growth Condition: none

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 880, 19640; Software: type: feature extraction; Performer: Regula,,Halbeisen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-04-04; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 420; Parameter Laser on time = 10162; Parameter Laser Power = 3.06; Parameter Scan Time = 11:51:58; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 23.81; Performer: Regula,,Halbeisen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-04-04; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 330; Parameter Scan Power = 100; Parameter Laser on time = 10162; Parameter Laser Power = 3.56; Parameter Scan Time = 11:51:58; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 23.81; Performer: Regula,,Halbeisen


title: AAs starvation RPL16a-ZZ total vs reference (5)

description:
Simple annotation: RNA coimmunoprecipitation, AA_starvation
Image: http://smd.stanford.edu/MicroArray/gifs/2006-08/69632.gif
Measurement: time(absolute) 20 m
Growth Condition: Amino acid starvation

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 840, 20000; Software: type: feature extraction; Performer: Regula,,Halbeisen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-08-09; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 390; Parameter Laser on time = 13952; Parameter Laser Power = 2.84; Parameter Scan Time = 12:03:45; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 25.81; Performer: Regula,,Halbeisen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-08-09; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 380; Parameter Scan Power = 100; Parameter Laser on time = 13952; Parameter Laser Power = 3.63; Parameter Scan Time = 12:03:45; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 25.81; Performer: Regula,,Halbeisen

source_name: Total RNA RPL16a-ZZ AA20

tag: Total RNA RPL16a-ZZ AA20


title: RPL16a-ZZ total vs reference (5)

description:
Simple annotation: RNA coimmunoprecipitation, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2006-08/69606.gif
Measurement: time(absolute) 0 m
Growth Condition: none

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 920, 20360; Software: type: feature extraction; Performer: Regula,,Halbeisen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-08-03; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 470; Parameter Laser on time = 13142; Parameter Laser Power = 2.97; Parameter Scan Time = 11:01:48; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 25.63; Performer: Regula,,Halbeisen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-08-03; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 420; Parameter Scan Power = 100; Parameter Laser on time = 13142; Parameter Laser Power = 3.64; Parameter Scan Time = 11:01:48; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 25.63; Performer: Regula,,Halbeisen


title: Rpl16a-ZZ Gradient (4)

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2009-01/82651.gif
Media: SC


title: AAs starvation RPL16a-ZZ IP poly vs reference (3)

description:
Simple annotation: RNA coimmunoprecipitation, AA_starvation
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67975.gif
Measurement: time(absolute) 10 m
Growth Condition: Amino acid starvation

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 760, 20000; Software: type: feature extraction; Performer: Regula,,Halbeisen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-04-04; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 430; Parameter Laser on time = 10313; Parameter Laser Power = 3.08; Parameter Scan Time = 14:22:36; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 24.69; Performer: Regula,,Halbeisen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-04-04; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 430; Parameter Scan Power = 100; Parameter Laser on time = 10312; Parameter Laser Power = 3.61; Parameter Scan Time = 14:22:36; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 24.69; Performer: Regula,,Halbeisen

source_name: IP RNA RPL16a-ZZ AA-starved

tag: IP RNA RPL16a-ZZ AA-starved


title: Rpl16a-ZZ Gradient (1)

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2009-01/82652.gif
Media: SC


title: Rpl16b-ZZ in SC (2)

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/80814.gif
Media: SC

source_name: Total RNA Rpl16b-ZZ

value: Total RNA Rpl16b-ZZ

source_name: IP RNA (RA) Rpl16b-ZZ

value: IP RNA (RA) Rpl16b-ZZ


title: Rpl16a-ZZ in SC (2)

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/80813.gif
Media: SC

source_name: IP RNA (RA) Rpl16a-ZZ

value: IP RNA (RA) Rpl16a-ZZ


title: AAs starvation RPL16a-ZZ IP poly vs reference (6)

description:
Simple annotation: RNA coimmunoprecipitation, AA_starvation
Image: http://smd.stanford.edu/MicroArray/gifs/2006-10/70714.gif
Measurement: time(absolute) 20 m
Growth Condition: Amino acid starvation

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1840, 19960; Software: type: feature extraction; Performer: Regula,,Halbeisen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-10-17; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 380; Parameter Laser on time = 15593; Parameter Laser Power = 2.95; Parameter Scan Time = 09:30:58; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 24.00; Performer: Regula,,Halbeisen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-10-17; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 360; Parameter Scan Power = 100; Parameter Laser on time = 15593; Parameter Laser Power = 3.59; Parameter Scan Time = 09:30:58; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 24.00; Performer: Regula,,Halbeisen


title: Rpl16b-ZZ in SC (1)

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/80812.gif
Media: SC


title: Rpl16a-ZZ in SC (1)

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/80811.gif
Media: SC


title: Infected sample number 10559

city: Ciudad Real

first: Ruth

middle: Cecilia

last: Galindo

state: Ciudad Real

address: Ronda de Toledo s/n

department: Animal Health

country: Spain

institute: Instituto de Investigacion en Recursos Cinegéticos

description:
1 year-old European wild boar male hunter-killed during 2007 in Kočevje–Šubičeva and Kostel–Delač, Slovenia
European wild boar non infected (Anaplasma phagocytophilum) Sample 10559

hyb_protocol: GeneChip® HT IVT Labeling Kit (Affymetrix)

scan_protocol: Microarray Analysis Suite 5.0

data_processing: Microarray data analysis was done using the free statistical language R and the libraries developed by the Bioconductor Project (www.bioconductor.org)

label: Biotin

organism: Sus scrofa

source_name: RNA white blood cells

label_protocol: Affymetrix two-cycle labeling protocol

extract_protocol: RNA was extracted using TRIzol Reagent (Invitrogen, Life Technologies Corporation, Carlsbad, California, USA)

treatment_protocol: European wild boar infected with Anaplasma phagocytophilum  sample 10559

tag: cell type

value: white blood cell

tag: disease state

value: Anaplasma phagocytophilum infected


title: Non-infected sample number 2

description:
Non infected sample number 2
European wild boar non infected (Anaplasma phagocytophilum) Sample 2

data_processing: Microarray data analysis was done using the free statistical language R and the libraries developed by the Bioconductor Project (www.bioconductor.org)The data were normalized with the RMA method.

source_name: RNA from white blood cells

extract_protocol: TRIzol Reagent (Invitrogen, Life Technologies Corporation, Carlsbad, California, USA)

value: uninfected


title: Infected sample number 10557

description:
Sample collected from 1 year-old European wild boar male hunter-killed during 2007 in Kočevje–Šubičeva and Kostel–Delač, Slovenia, infected with Anaplasma phagocytophilum.
European wild boar non infected (Anaplasma phagocytophilum) Sample 10557

treatment_protocol: European wild boar infected with Anaplasma phagocytophilum


title: Rpl16a-ZZ Gradient (2)

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2009-01/82653.gif
Media: SC


title: Non-infected sample number 10

description:
Non infected sample Number 2
European wild boar non infected (Anaplasma phagocytophilum) Sample 2

data_processing: Microarray data analysis was done using the free statistical language R and the libraries developed by the Bioconductor Project (www.bioconductor.org).  The data were normalized with the RMA method.The data were normalized with the RMA method.

source_name: RNA  from white blood cells


title: Non-infected sample number 5

description:
Non infected sample number 5
European wild boar non infected (Anaplasma phagocytophilum) Sample 5

data_processing: Microarray data analysis was done using the free statistical language R and the libraries developed by the Bioconductor Project (www.bioconductor.org) The data were normalized with the RMA method.


title: CHM117Nsp

type: genomic

city: Fukuoka

first: Kenshi

last: Hayashi

address: Maidashi 3-1-1, Higashi-ku

department: Medical Institute of Bioregulation

country: Japan

institute: Kyushu University

hyb_protocol: Hybridizations were performed according to the standard Affymetrix protocol using an Affymetrix hybridisation oven 640 and an Affymetrix Fluidic station 450.

scan_protocol: Genechips were scanned using Gene Chip Scanner 3000 7G and Gene Chip Operating System.

data_processing: CEL and CHP files were processed by Affymetrix GCOS 1.4 with default analysis settings. Calls were generated by Affymetrix GTYPE 4.0 using the DM algorithm with confidence threshold 0.33.

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: complete hydatidiform mole

label_protocol: Biotinylated DNA was prepared according to the standard Affymetrix protocol from 250 ng genomic DNA.

extract_protocol: QIAamp DNA Mini Kit (Qiagen).

tag: complete hydatidiform moles


title: CHM102Nsp


title: CHM111Nsp


title: CHM116Nsp


title: CHM108Nsp


title: CHM110Nsp


title: CHM115Nsp


title: CHM105Nsp


title: CHM101Nsp


title: CHM098Nsp


title: P210_tp 3_biological replicate 2

city: Lund

first: Petra

last: Johnels

address: Lund University Hospital

department: Clinical Genetics

country: Sweden

institute: Lund University

description: oligo microarray data

hyb_protocol: Arrays were hybridized and washed as described (Järås et al., 20089, Exp Hematol)

scan_protocol: Arrays were scanned in an Agilent Microarray scanner

data_processing: Spot quality was analyzed with GenePix 4.0 software. Raw data were normalized (pin-based Lowess regression) and filtered (SNR > 2, SD >= 0.2, presence >= 90%) in the BioArray Software Environment (BASE).

source_name: CD34+ cells expressing P210 BCR/ABL1, 4 days post transduction, replicate 2

label_protocol: Samples were labeled using the Agilent low RNA input fluorescent linear amplification kit (Agilent Technologies)

growth_protocol: cells were grown as described (Järås et al., 2009, Exp Hematol)

extract_protocol: Trizol extraction followed by purification using RNeasy

value: CD34+ cord blood cells expressing P210 BCR/ABL1

tag: time

value: 4 days post transduction

tag: sample type

value: P210 BCR/ABL1

source_name: Stratagene Universal Human Reference RNA

value: RNA pooled from ten human cell lines


title: CHM100Nsp


title: P210_tp 2_biological replicate 2

description: oligo microarray data

source_name: CD34+ cells expressing P210 BCR/ABL1, 3 days post transduction, replicate 2

value: 3 days post transduction


title: CHM113Nsp


title: CHM099Nsp


title: CHM114Nsp


title: P210_tp 1_biological replicate 2

description: oligo microarray data

source_name: CD34+ cells expressing P210 BCR/ABL1, 2 days post transduction, replicate 2

value: 2 days post transduction


title: CHM104Nsp


title: P190_tp 3_biological replicate 2

description: oligo microarray data

source_name: CD34+ cells expressing P190 BCR/ABL1, 4 days post transduction, replicate 2

value: CD34+ cord blood cells expressing P190 BCR/ABL1

value: P190 BCR/ABL1


title: CHM093Nsp


title: CHM094Nsp


title: CHM106Nsp


title: CHM088Nsp


title: CHM103Nsp


title: P190_tp 2_biological replicate 2

description: oligo microarray data

source_name: CD34+ cells expressing P190 BCR/ABL1, 3 days post transduction, replicate 2


title: P190_tp 1_biological replicate 2

description: oligo microarray data

source_name: CD34+ cells expressing P190 BCR/ABL1, 2 days post transduction, replicate 2


title: CHM095Nsp


title: CHM090Nsp


title: MIG_tp 3_biological replicate 2

description: oligo microarray data

source_name: CD34+ control cells, 4 days post transduction, replicate 2

value: CD34+ cord blood cells

value: control


title: MIG_tp 2_biological replicate 2

description: oligo microarray data

source_name: CD34+ control cells, 3 days post transduction, replicate 2


title: CHM097Nsp


title: P210_tp 3_biological replicate 1

description: oligo microarray data

source_name: CD34+ cells expressing P210 BCR/ABL1, 4 days post transduction, replicate 1


title: MIG_tp 1_biological replicate 2

description: oligo microarray data

source_name: CD34+ control cells, 2 days post transduction, replicate 2


title: CHM087Nsp


title: P210_tp 2_biological replicate 1

description: oligo microarray data

source_name: CD34+ cells expressing P210 BCR/ABL1, 3 days post transduction, replicate 1


title: control, biological rep1

city: Rensselaer

first: Sridar

middle: V

last: Chittur

state: NY

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

country: USA

institute: SUNY-University at Albany

description: Gene expression data from control tissue

hyb_protocol: Std Affymetrix 1 cycle

scan_protocol: Std Affymetrix 1 cycle

organism: Canis lupus familiaris

source_name: Left ventricle

label_protocol: Std Affymetrix 1 cycle

growth_protocol: Not applicable

extract_protocol: Qiagen RNEasy with on-column DNAse

treatment_protocol: tissue frozen in liq N2 was used

tag: tissue

value: heart, left ventricle

tag: age

tag: gender

value: male

tag: breed

value: Labrador retriever


title: P210_tp 1_biological replicate 1

description: oligo microarray data

source_name: CD34+ cells expressing P210 BCR/ABL1, 2 days post transduction, replicate 1


title: diseased, biological rep2

description: Gene expression data from DCM tissue

value: Great Dane


title: P190_tp 3_biological replicate 1

description: oligo microarray data

source_name: CD34+ cells expressing P190 BCR/ABL1, 4 days post transduction, replicate 1


title: control, biological rep3

value: Greater Swiss Mountain dog


title: diseased, biological rep1

description: Gene expression data from DCM tissue

value: female


title: diseased, biological rep3

description: Gene expression data from DCM tissue


title: control, biological rep2

value: St. Bernard


title: CHM086Nsp


title: P190_tp 2_biological replicate 1

description: oligo microarray data

source_name: CD34+ cells expressing P190 BCR/ABL1, 3 days post transduction, replicate 1


title: P190_tp 1_biological replicate 1

description: oligo microarray data

source_name: CD34+ cells expressing P190 BCR/ABL1, 2 days post transduction, replicate 1


title: CHM084Nsp

source_name: complete hydatidiform mole


title: MIG_tp 3_biological replicate 1

description: oligo microarray data

source_name: CD34+ control cells, 4 days post transduction, replicate 1

source_name: Stratagene Universal Human Reference RNA


title: CHM085Nsp


title: CHM083Nsp


title: CHM116Sty


title: CHM082Nsp


title: MIG_tp 2_biological replicate 1

description: oligo microarray data

source_name: CD34+ control cells, 3 days post transduction, replicate 1


title: CHM076Nsp


title: CHM079Nsp


title: CHM117Sty


title: MIG_tp 1_biological replicate 1

description: oligo microarray data

source_name: CD34+ control cells, 2 days post transduction, replicate 1


title: CHM075Nsp


title: CHM081Nsp


title: CHM110Sty


title: CHM074Nsp


title: CHM111Sty


title: CHM078Nsp


title: CHM114Sty


title: CHM073Nsp


title: CHM108Sty


title: CHM070Nsp


title: CHM080Nsp


title: PBLs_pair 48695_unaffected

city: Chapel Hill

first: Patrick

middle: F

last: Sullivan

state: NC

address: 4109D Neuroscience Research Building, 103 Mason Farm Road

department: Genetics

institute: UNC Chapel Hill

description: gene expression data from PBLs, pair 48695, unaffected, female

hyb_protocol: Fragmented and labeled targets (together with hybridization and oligo B2 controls) were hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays at 45°C for 16 hours. Washing and staining of the arrays were performed on the Affymetrix fluidics station using the EukGE-WS2v5_450 protocol.

scan_protocol: Imaging of the arrays and signal quantification were performed with the Affymetrix GeneChip Scanner 3000 and GeneChip Operating Software. For verification, we used qRT-PCR. RNA was converted to cDNA with Superscript III (Invitrogen) and qRT-PCR was run with ABI's Taqman gene expression assays (with 18S rRNA as control). The ΔΔCt method was used for the calculations.

data_processing: Array images were manually checked for defects using DChip and then normalized using the RMA algorithm in Affymetrix Expression Console (v1.0). After normalization, the Bioconductor Significance Analysis of Microarrays package was used to compute modified paired t-tests that contrasted an affected twin with the unaffected co-twin for each transcript using R. To adjust for multiple comparisons, the nominal permutation-based p-values from SAM were used to compute false discovery rate q-values.

source_name: PBLs, pair 48695, unaffected

label_protocol: Total RNA (5.0 μg) was labeled with the one-cycle cDNA synthesis kit (Invitrogen) and spiked with eukaryotic Poly-A RNA controls to check the target labeling process (Affymetrix). Synthesized cDNA was transcribed in vitro using the GeneChip IVT labeling kit (Affymetrix). The biotin labeled cRNA product (20 μg) was purified with a sample cleanup module (Qiagen) and samples were fragmented with the fragmentation buffer from Affymetrix at 94°C for 35 minutes.

extract_protocol: Peripheral venous blood was drawn using sterile technique into PAXgene tubes manufactured in the same batch (Qiagen, to protect RNA from degradation and to minimize ex vivo gene expression). Total RNA was purified using the PAXgene blood RNA kit following the manufacturer’s instructions (Qiagen). RNA quality was determined using the Agilent 2100 Bioanalyzer.

tag: twin pair

tag: sex

tag: diagnonsis

value: unaffected


title: CHM113Sty


title: CHM115Sty


title: PBLs_pair 48695_ICF

description: gene expression data from PBLs, pair 48695, ICF, female

source_name: PBLs, pair 48695, ICF

value: ICF


title: PBLs_pair 236175_CFS

description: gene expression data from PBLs, pair 236175, CFS, male

source_name: PBLs, pair 236175, CFS

value: CFS


title: CHM072Nsp


title: PBLs_pair 236175_unaffected

description: gene expression data from PBLs, pair 236175, unaffected, male

source_name: PBLs, pair 236175, unaffected


title: CHM105Sty


title: CHM106Sty


title: CHM069Nsp


title: PBLs_pair 253644_unaffected

description: gene expression data from PBLs, pair 253644, unaffected, female

source_name: PBLs, pair 253644, unaffected


title: CHM104Sty


title: CHM103Sty


title: CHM067Nsp


title: PBLs_pair 253644_CFS

description: gene expression data from PBLs, pair 253644, CFS, female

source_name: PBLs, pair 253644, CFS


title: CHM101Sty


title: CHM099Sty


title: CHM068Nsp


title: CHM102Sty


title: PBLs_pair 33004_unaffected

description: gene expression data from PBLs, pair 33004, unaffected, female

source_name: PBLs, pair 33004, unaffected


title: CHM097Sty


title: CHM098Sty


title: CHM093Sty


title: CHM100Sty


title: CHM095Sty


title: CHM065Nsp


title: PBLs_pair 33004_CFS

description: gene expression data from PBLs, pair 33004, CFS, female

source_name: PBLs, pair 33004, CFS


title: CHM066Nsp


title: CHM094Sty


title: PBLs_pair 218156_unaffected

description: gene expression data from PBLs, pair 218156, unaffected, female

source_name: PBLs, pair 218156, unaffected


title: CHM088Sty


title: CHM064Nsp


title: CHM063Nsp


title: PBLs_pair 42935_unaffected

description: gene expression data from PBLs, pair, 42935, unaffected, female

source_name: PBLs, pair, 42935, unaffected


title: CHM090Sty


title: PBLs_pair 42935_CFS

description: gene expression data from PBLs, pair 42935, CFS, female

source_name: PBLs, pair 42935, CFS


title: CHM085Sty


title: CHM086Sty


title: CHM087Sty


title: PBLs_pair 226594_unaffected

description: gene expression data from PBLs, pair 226594, unaffected, female

source_name: PBLs, pair 226594, unaffected


title: CHM082Sty

source_name: complete hydatidiform mole


title: CHM061Nsp


title: PBLs_pair 226594_ICF

description: gene expression data from PBLs, pair 226594, ICF, female

source_name: PBLs, pair 226594, ICF


title: PBLs_pair 218156_CFS

description: gene expression data from PBLs, pair 218156, CFS, female

source_name: PBLs, pair 218156, CFS


title: PBLs_pair 249806_unaffected

description: gene expression data from PBLs, pair 249806, unaffected, female

source_name: PBLs, pair 249806, unaffected


title: CHM060Nsp


title: CHM084Sty


title: CHM083Sty


title: CHM080Sty


title: CHM081Sty


title: PBLs_pair 249806_ICF

description: gene expression data from PBLs, pair 249806, ICF, female

source_name: PBLs, pair 249806, ICF


title: CHM058Nsp


title: CHM059Nsp


title: CHM076Sty


title: PBLs_pair 3384_unaffected

description: gene expression data from PBLs, pair 3384, unaffected, male

source_name: PBLs, pair 3384, unaffected


title: CHM079Sty


title: CHM057Nsp


title: PBLs_pair 3384_CFS

description: gene expression data from PBLs, pair 3384, CFS, male

source_name: PBLs, pair 3384, CFS


title: PBLs_pair 31148_CFS

description: gene expression data from PBLs, pair 31148, CFS, female

source_name: PBLs, pair 31148, CFS


title: CHM078Sty


title: CHM054Nsp


title: CHM056Nsp


title: CHM074Sty


title: PBLs_pair 31148_unaffected

description: gene expression data from PBLs, pair 31148, unaffected, female

source_name: PBLs, pair 31148, unaffected


title: CHM075Sty


title: PBLs_pair 246763_CFS

description: gene expression data from PBLs, pair 246763, CFS, female

source_name: PBLs, pair 246763, CFS


title: CHM055Nsp


title: PBLs_pair 246763_unaffected

description: gene expression data from PBLs, pair 246763, unaffected, female

source_name: PBLs, pair 246763, unaffected


title: CHM053Nsp


title: mouse324_vs_male_pool: muscle

status: Public on Aug 31 2009

city: Toronto

first: Tomas

last: Babak

state: ON

address: 112 College St

department: Banting and Best Department of Medical Research

country: Canada

institute: Best Institute

hyb_protocol: The hybridizations were performed to single arrays (individuals F2 samples labeled with Cy5 and reference pools labeled with Cy3 fluorochromes) for 24 h in a hybridization chamber, washed, and scanned using a confocal laser scanner. Arrays were quantified on the basis of spot intensity relative to background, adjusted for experimental variation between arrays using average intensity over multiple channels, and fitted to a previously described error model to determine significance21 (type I error)

scan_protocol: Standard dual-channel Agilent scanner with manufacturer provided software.

data_processing: See Rosetta Error Model (PMID: 16522673)

molecule: polyA RNA

organism: Mus musculus

source_name: mouse324, muscle

label_protocol: Three micrograms of total RNA was reverse transcribed and labeled with either Cy3 or Cy5 fluorochrome. Labeled complementary RNA (cRNA) from each F2 animal was hybridized against a cross-specific pool of labeled cRNAs constructed from equal aliquots of RNA from 150 F2 animals and parental mouse strains for each of the three tissues.

growth_protocol: All mice were maintained on a 12 h light–12 h dark cycle and fed ad libitum. Mice were fed Purina Chow until 10 wk of age, and then fed western diet (Teklad 88137, Harlan Teklad) for the subsequent 8 wk.

extract_protocol: Mouse tissues were homogenized, and total RNA extracted using Trizol reagent (Invitrogen) according to manufacturer's protocol.

treatment_protocol: Mice were fasted overnight before they were killed. Their tissues were collected, flash frozen in liquid nitrogen, and stored in −80 °C prior to RNA isolation.  All procedures of housing and treatment of animals were performed in accordance with Institutional Animal Care and Use Committee regulations.

tag: strain

value: CAST/EiJ x C57BL/6J

tag: treatment category

value: test sample

value: muscle

source_name: reference pool (male, muscle)

value: reference pool


title: PBLs_pair 32691_ICF

description: gene expression data from PBLs, pair 32691, ICF, female

source_name: PBLs, pair 32691, ICF


title: mes-2 embryo, 2E stage, Replicate 2

status: Public on May 26 2009

city: Salt Lake City

first: Susan

last: Mango

state: UT

address: 2000 Circle of Hope

department: Oncological Sciences

institute: University of Utah

description: total RNA from a single embryos

hyb_protocol: Fluorescently labeled cRNA samples (825 ng each) were fragmented and combined with Agilent Hi-RPM Hybridization Buffer.  Microarray hybridizations were performed using Agilent SureHyb Hybridization chambers.  Hybridization chambers were loaded onto a rotisserie in an Agilent Hybridization oven and were incubated at 65ºC for 17 hours with a rotational speed of 10 rpm.  Following incubation, the microarray slide was washed for 1 minute each in Gene Expression Wash Buffer 1 (6X SSPE, 0.005% N-lauroylsarcosine; room temperature) and Gene Expression Wash Buffer (0.06X SSPE, 0.005% N-lauroylsarcosine; 31ºC) for 1 minute each.  Microarray slides were briefly dipped in a solution of acetonitrile and dried.

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505B Microarray Scanner at 5 µm resolution.  The scanner performs simultaneous detection of Cyanine-3 and Cyanine-5 signal on the hybridized slide.  Data captured from the scanned microarray image is saved as a TIF file.

data_processing:
TIF image files were processed with Agilent Feature Extraction Software version 9.5.1.
Non-uniform features were discarded and features with the same probe were averaged. Mean spot intensity was log (base 2) transformed and quantile normalized within groups. Group medians were adjusted to be equal.

organism: Caenorhabditis elegans

source_name: Cy3_WT mix embryos; Cy5_mes-2 2E single embryo

label_protocol: PCR-amplified DNA samples (2-3 µg) derived from chromatin immunoprecipitation reactions were labeled using the Agilent Genomic DNA Labeling Kit PLUS.  The labeling kit uses random primers and the exo-Klenow fragment to label DNA through incorporation of fluorescently labeled nucleotides (Cy3-dUTP or Cy5-dUTP).  Following termination of the labeling reaction, fluorescently labeled DNA molecules were purified by isopropanol precipitation.  Precipitated pellets were dried and then rehydrated in distilled water.  The concentration of purified samples was determined using a NanoDrop ND-1000 spectrophotometer.  A fraction of the labeled DNA (100 ng) was run on an Agilent BioAnalyzer to validate the size distribution of the labeled DNA molecules.

growth_protocol: 2-cell embryos were collected from wild-type or mes-2 mothers and incubated at 20°C for 75 min. (2E), 120 min. (4E), 3h. (8E).

extract_protocol: cDNA from individual embryos was isolated as described (Robertson et al., 2004). Briefly, individual embryos were placed in 0.5 $B&L (Bl of cDNA 1st-strand buffer (Robertson et al., 2004), squashed with a small piece of coverslip and immediately frozen on dry ice. Upon thawing, 4 $B&L (Bl of 1st -strand buffer was added to each embryo. After heating to 65 °C (BC for 90 s, the tube was cooled to 45 °C (BC and reverse transcription initiated with the addition of 0.5 $B&L (Bl Superscript III. After 60 min, the reaction was terminated by heating to 70 °C (BC for 15 min, 0.5 $B&L (Bl RNAse H was added and RNA digested at 37 °C (BC for 20 min. The cDNA strands were polyA tailed by the addition of 5 $B&L (Bl of 2 $B!_ (B TdT buffer containing dATP, and terminal deoxynucleotidyl transferase, and incubated at 37 °C (BC for 15 min. Tailing was stopped by heating to 65 °C (BC for 10 min. 40 °C (Bl of PCR buffer was added to each tube followed by 50 cycles of PCR amplification. This primary RT-PCR amplification product could then be reamplified as needed to generate more total cDNA.

tag: strain (cy3)

tag: strain (cy5)


title: CHM073Sty


title: PBLs_pair 32691_unaffected

description: gene expression data from PBLs, pair 32691, unaffected, female

source_name: PBLs, pair 32691, unaffected


title: CHM072Sty


title: CHM050Nsp


title: PBLs_pair 31885_ICF

description: gene expression data from PBLs, pair 31885, ICF, female

source_name: PBLs, pair 31885, ICF


title: CHM069Sty

source_name: complete hydatidiform mole


title: PBLs_pair 31885 unaffected

description: gene expression data from PBLs, pair 31885 unaffected, female

source_name: PBLs, pair 31885 unaffected


title: UPN44S_AML

status: Public on May 28 2009

city: Nijmegen

first: Roland

middle: P.

last: Kuiper

address: Geert Grooteplein 10

department: Human Genetics

country: Netherlands

institute: Radboud University Nijmegen Medical Centre

description: primary AML diagnosis sample

hyb_protocol: Hybridizations were performed according to the standard Affymetrix protocol from two times 250 ng genomic DNA (Genome-Wide Human SNP Nsp/Sty 6.0 User Guide manual 702504 Rev.1, Affymetrix) using an Affymetrix hybridisation oven 640 and an Affymetrix Fluidic station 450.

scan_protocol: Scanning performed according to the standard Affymetrix protocol from two times 250 ng genomic DNA ((Genome-Wide Human SNP Nsp/Sty 6.0 User Guide manual 702504 Rev.1, Affymetrix) using an Affymetrix scanner 3000.

data_processing: CNAG 2.0 and Affymetrix Genotypic Console 2.1

source_name: Bone marrow

label_protocol: Biotinylated DNA was prepared according to the standard Affymetrix protocol from two times 250 ng genomic DNA (Genome-Wide Human SNP Nsp/Sty 6.0 User Guide manual 702504 Rev.1, Affymetrix).

extract_protocol: QiaAmp purification kit (Qiagen)

value: Bone marrow

value: MDS

tag: sample

value: AML diagnosis sample


title: CHM070Sty


title: PBLs_pair 31657_CFS

description: gene expression data from PBLs, pair 31657, CFS, female

source_name: PBLs, pair 31657, CFS


title: CHM068Sty


title: CHM051Nsp


title: CHM047Nsp


title: PBLs_pair 31657_unaffected

description: gene expression data from PBLs, pair 31657, unaffected, female

source_name: PBLs, pair 31657, unaffected


title: CHM048Nsp


title: CHM066Sty


title: CHM065Sty


title: CHM062Nsp


title: PBLs_pair 253224_ICF

description: gene expression data from PBLs, pair 253224, ICF, female

source_name: PBLs, pair 253224, ICF


title: CHM049Nsp


title: PBLs_pair 253224_unaffected

description: gene expression data from PBLs, pair 253224, unaffected, female

source_name: PBLs, pair 253224, unaffected


title: CHM042Nsp


title: CHM043Nsp


title: CHM067Sty


title: CHM061Sty


title: CHM063Sty


title: Vein endothelial cells_Young_Static_rep3

status: Public on May 23 2009

city: Daegu

first: Yong Chool

last: Boo

address: 101 Dongindong

department: Department of Molecular Medicine

country: South Korea

institute: Kyungpook National University School of Medicine

description: Replicate 3 of 3

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 7G.

data_processing: The MAS5 algorithm was used for expression summary and signal calculation of Affymetrix Human Genome U133 Plus 2.0 data. Global scaling normalization was performed and then the normalized data were log-transformed with base 2.

source_name: Human umbilical vein endothelial cells, young, static

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: HUVECs purchased from Clonetics Cambrex (Rockland, ME, USA) were cultured on 0.2% gelatin-coated 100-mm tissue culture dishes (BD Biosciences, San Jose, CA, USA) at 37 °C and 5% CO2 in endothelial cell growth medium EBM-2 (Clonetics Cambrex) with endothelial growth supplements and 10% fetal bovine serum (Gibco BRL, Grand Island, NY, USA).

extract_protocol: Total RNA extraction with Qiagen RNeasy mini kit was performed according to the manufacturer's instructions.

treatment_protocol: Cells were serially passaged until they showed phenotypes of senescence. Young (p4) and senescent (p18) cells grown on 100 mm culture dishes were exposed to laminar shear stress at 12 dyn•cm-2 for 24 hours. Laminar shear stress was provided by rotating a Teflon cone (0.5° cone angle) mounted onto a culture dish.

tag: young (p4)


title: PBLs_pair 44110_CFS

description: gene expression data from PBLs, pair 44110, CFS, female

source_name: PBLs, pair 44110, CFS


title: CHM062Sty


title: CHM046Nsp


title: CHM041Nsp


title: PBLs_pair 4334_CFS

description: gene expression data from PBLs, pair 4334, CFS, female

source_name: PBLs, pair 4334, CFS


title: CHM036Nsp


title: PBLs_pair 4122_CFS

description: gene expression data from PBLs, pair 4122, CFS, female

source_name: PBLs, pair 4122, CFS


title: CHM064Sty


title: PBLs_pair 4122_unaffected

description: gene expression data from PBLs, pair 4122, unaffected, female

source_name: PBLs, pair 4122, unaffected


title: CHM060Sty


title: CHM059Sty


title: CHM057Sty


title: PBLs_pair 4334_unaffected

description: gene expression data from PBLs, pair 4334, unaffected, female

source_name: PBLs, pair 4334, unaffected


title: CHM034Nsp


title: PBLs_pair 248659_CFS

description: gene expression data from PBLs, pair 248659, CFS, female

source_name: PBLs, pair 248659, CFS


title: PBLs_pair 248659_unaffected

description: gene expression data from PBLs, pair 248659, unaffected, female

source_name: PBLs, pair 248659, unaffected


title: PBLs_pair 44110_unaffected

description: gene expression data from PBLs, pair 44110, unaffected, female

source_name: PBLs, pair 44110, unaffected


title: CHM056Sty


title: CHM039Nsp


title: PBLs_pair 247956_unaffected

description: gene expression data from PBLs, pair 247956, unaffected, male

source_name: PBLs, pair 247956, unaffected


title: CHM033Nsp

source_name: complete hydatidiform mole


title: CHM035Nsp


title: CHM032Nsp


title: PBLs_pair 247956_CFS

description: gene expression data from PBLs, pair 247956, CFS, male

source_name: PBLs, pair 247956, CFS


title: PBLs_pair 246138_unaffected

description: gene expression data from PBLs, pair 246138, unaffected, female

source_name: PBLs, pair 246138, unaffected


title: CHM055Sty


title: CHM030Nsp


title: PBLs_pair 246138_CFS

description: gene expression data from PBLs, pair 246138, CFS, female

source_name: PBLs, pair 246138, CFS


title: CHM058Sty


title: PBLs_pair 222171_unaffected

description: gene expression data from PBLs, pair 222171, unaffected, female

source_name: PBLs, pair 222171, unaffected


title: CHM051Sty


title: CHM053Sty


title: CHM029Nsp


title: CHM026Nsp


title: CHM038Nsp


title: CHM040Nsp


title: CHM049Sty


title: PBLs_pair 244184_unaffected

description: gene expression data from PBLs, pair 244184, unaffected, female

source_name: PBLs, pair 244184, unaffected


title: PBLs_pair 244184_CFS

description: gene expression data from PBLs, pair 244184, CFS, female

source_name: PBLs, pair 244184, CFS


title: PBLs_pair 222171_ICF

description: gene expression data from PBLs, pair 222171, ICF, female

source_name: PBLs, pair 222171, ICF


title: CHM050Sty


title: CHM048Sty


title: PBLs_pair 235566_unaffected

description: gene expression data from PBLs, pair 235566, unaffected, female

source_name: PBLs, pair 235566, unaffected


title: CHM046Sty


title: CHM031Nsp


title: CHM023Nsp


title: CHM028Nsp


title: PBLs_pair 235566_CFS

description: gene expression data from PBLs, pair 235566, CFS, female

source_name: PBLs, pair 235566, CFS


title: CHM022Nsp


title: CHM043Sty


title: CHM019Nsp


title: CHM021Nsp


title: PBLs_pair 232629_unaffected

description: gene expression data from PBLs, pair 232629, unaffected, female

source_name: PBLs, pair 232629, unaffected


title: PBLs_pair 232629_CFS

description: gene expression data from PBLs, pair 232629, CFS, female

source_name: PBLs, pair 232629, CFS


title: CHM018Nsp


title: CHM024Nsp


title: CHM042Sty


title: PBLs_pair 228991_ICF

description: gene expression data from PBLs, pair 228991, ICF, female

source_name: PBLs, pair 228991, ICF


title: CHM047Sty


title: PBLs_pair 233889_CFS

description: gene expression data from PBLs, pair 233889, CFS, female

source_name: PBLs, pair 233889, CFS


title: PBLs_pair 233889_unaffected

description: gene expression data from PBLs, pair 233889, unaffected, female

source_name: PBLs, pair 233889, unaffected


title: CHM040Sty


title: CHM036Sty


title: CHM038Sty


title: CHM039Sty


title: CHM041Sty


title: PBLs_pair 228991_unaffected

description: gene expression data from PBLs, pair 228991, unaffected, female

source_name: PBLs, pair 228991, unaffected


title: CHM015Nsp


title: CHM034Sty


title: CHM014Nsp


title: CHM013Nsp


title: PBLs_pair 217666_CFS

description: gene expression data from PBLs, pair 217666, CFS, female

source_name: PBLs, pair 217666, CFS


title: PBLs_pair 217666_unaffected

description: gene expression data from PBLs, pair 217666, unaffected, female

source_name: PBLs, pair 217666, unaffected


title: CHM011Nsp

source_name: complete hydatidiform mole


title: PBLs_pair 228030_CFS

description: gene expression data from PBLs, pair 228030, CFS, female

source_name: PBLs, pair 228030, CFS


title: CHM033Sty


title: CHM020Nsp


title: PBLs_pair 228030_unaffected

description: gene expression data from PBLs, pair 228030, unaffected, female

source_name: PBLs, pair 228030, unaffected


title: PBLs_pair 212940_CFS

description: gene expression data from PBLs, pair 212940, CFS, female

source_name: PBLs, pair 212940, CFS


title: CHM012Nsp


title: CHM031Sty


title: CHM010Nsp


title: CHM007Nsp


title: CHM030Sty


title: CHM035Sty


title: 10mg/kg/day PFOS, liver rep5

city: Research Triangle Park

first: Mitchell

middle: B

last: Rosen

department: Reproductive Toxicology

institute: U.S. EPA

description: Fetal liver gene expression data from full term pups exposed to PFOS throughout gestation.

hyb_protocol: Following fragmentation, samples were hybridized overnight at 45C according to the protocols recommended by the manufacturer in an Affymetrix Model 640 GeneChip hybridization oven

scan_protocol: The arrays were washed and stained using an Affymetrix 450 fluidics station as recommended by the manufacturer, and scanned on an Affymetrix Model 3000 scanner.

data_processing: Probe set data were summarized, background adjusted, and quantile normalized using Robust Multichip Average methodology (Irizarry et al., 2003) as provided by RMA Express (version 0.4).

source_name: Fetal liver, CD-1 background

label_protocol: Biotin-labeled cRNA was produced from 2 ug total RNA using the Affymetrix one-way labeling kit (cat# 900493).

extract_protocol: Collected tissue was immediately homogenized in TRI reagent and processed on the same day through alcohol precipitation according to the manufacturerÆs directions. RNA pellets were then washed in cold 80% ethanol and stored at -80C until further use.  Following resuspension in nuclease-free water, the RNA was quantified and evaluated for purity (260nm/280nm ratio) using a NanoDrop ND-1000 spectrophotometer. 100 ug of each sample was then further purified using RNeasy spin columns according to the manufacturerÆs directions. Approximately 250 ng of each sample was evaluated for quality using an Agilent 2100 Bioanalyzer.  RNA samples were used only if they were found to have an RNA Integrity Number of at least 8.0.

treatment_protocol: Timed-pregnant CD-1 mice were dosed by oral gavage from gestation day (GD)1 through GD 17 with PFOS (potassium salt) prepared fresh each day in 0.5% Tween 20.  The presence of a sperm plug was considered GD 0.   On GD18, dams were euthanized by CO2 asphyxiation and three fetuses per litter were collected for preparation of total RNA from a portion of the liver and lung.

tag: Pooled litter samples were collected 24 hrs after the final compound dose.


title: PBLs_pair 212940_unaffected

description: gene expression data from PBLs, pair 212940, unaffected, female

source_name: PBLs, pair 212940, unaffected


title: CHM009Nsp

tag: complete hydatidiform moles


title: PBLs_pair 229213_unaffected

description: gene expression data from PBLs, pair 229213, unaffected, female

source_name: PBLs, pair 229213, unaffected


title: 10mg/kg/day PFOS, liver rep4


title: CHM008Nsp


title: CHM032Sty


title: PBLs_pair 229213_ICF

description: gene expression data from PBLs, pair 229213, ICF, female

source_name: PBLs, pair 229213, ICF


title: 10mg/kg/day PFOS, lung rep4

description: Fetal lung gene expression data from full term pups exposed to PFOS throughout gestation.

source_name: Fetal lung, CD-1 background


title: 10mg/kg/day PFOS, liver rep3


title: PBLs_pair 239142_CFS

description: gene expression data from PBLs, pair 239142, CFS, male

source_name: PBLs, pair 239142, CFS


title: 10mg/kg/day PFOS, lung rep5


title: CHM006Nsp


title: PBLs_pair 239142_unaffected

description: gene expression data from PBLs, pair 239142, unaffected, male

source_name: PBLs, pair 239142, unaffected


title: CHM054Sty


title: CHM028Sty


title: PBLs_pair 240094_unaffected

description: gene expression data from PBLs, pair 240094, unaffected, female

source_name: PBLs, pair 240094, unaffected


title: 10mg/kg/day PFOS, lung rep2


title: 10mg/kg/day PFOS, liver rep2


title: 10mg/kg/day PFOS, liver rep1


title: PBLs_pair 244484_unaffected

description: gene expression data from PBLs, pair 244484, unaffected, female

source_name: PBLs, pair 244484, unaffected


title: CHM026Sty


title: PBLs_pair 240094_ICF

description: gene expression data from PBLs, pair 240094, ICF, female

source_name: PBLs, pair 240094, ICF


title: PBLs_pair 244484_CFS

description: gene expression data from PBLs, pair 244484, CFS, female

source_name: PBLs, pair 244484, CFS


title: CHM023Sty


title: 10mg/kg/day PFOS, lung rep1


title: CHM020Sty


title: CHM022Sty


title: CHM002Nsp


title: 5mg/kg/day PFOS, liver rep5

source_name: Fetal liver CD-1 background


title: 5mg/kg/day PFOS, liver rep4


title: PBLs_pair 244431_CFS

description: gene expression data from PBLs, pair 244431, CFS, female

source_name: PBLs, pair 244431, CFS


title: CHM003Nsp

source_name: complete hydatidiform mole


title: 5mg/kg/day PFOS, lung rep5

source_name: Fetal lung CD-1 background


title: CHM024Sty


title: PBLs_pair 244431_unaffected

description: gene expression data from PBLs, pair 244431, unaffected, female

source_name: PBLs, pair 244431, unaffected


title: PBLs_pair 220062_CFS

description: gene expression data from PBLs, pair 220062, CFS, female

source_name: PBLs, pair 220062, CFS


title: 10mg/kg/day PFOS, lung rep3


title: CHM019Sty


title: 5mg/kg/day PFOS, lung rep4


title: PBLs_pair 234559_unaffected

description: gene expression data from PBLs, pair 234559, unaffected, female

source_name: PBLs, pair 234559, unaffected


title: CHM001Nsp


title: CHM018Sty


title: CHM005Nsp


title: 5mg/kg/day PFOS, liver rep3

source_name: Fetal liver, CD-1 background


title: 5mg/kg/day PFOS, liver rep2


title: PBLs_pair 239415_CFS

description: gene expression data from PBLs, pair 239415, CFS, female

source_name: PBLs, pair 239415, CFS


title: PBLs_pair 234559_CFS

description: gene expression data from PBLs, pair 234559, CFS, female

source_name: PBLs, pair 234559, CFS


title: 5mg/kg/day PFOS, lung rep3

source_name: Fetal lung, CD-1 background


title: 5mg/kg/day PFOS, lung rep2


title: CHM016Nsp


title: CHM021Sty


title: PBLs_pair 239415_unaffected

description: gene expression data from PBLs, pair 239415, unaffected, female

source_name: PBLs, pair 239415, unaffected


title: CHM014Sty


title: CHM029Sty


title: CHM015Sty


title: 5mg/kg/day PFOS, liver rep1

description: Fetal liver gene expression data from full term pups exposed to PFOS throughout gestation.


title: 5mg/kg/day PFOS, lung rep1


title: CHM016Sty


title: CHM013Sty


title: CHM012Sty


title: PBLs_pair 230813_CFS

description: gene expression data from PBLs, pair 230813, CFS, female

source_name: PBLs, pair 230813, CFS


title: CHM010Sty


title: PBLs_pair 220062_unaffected

description: gene expression data from PBLs, pair 220062, unaffected, female

source_name: PBLs, pair 220062, unaffected


title: MCF7 1uM 24h

city: Stockholm

first: Martin

last: Enge

address: CCK, Z4

department: Dep of Oncology-Pathology

institute: Karolinska Institute

description: Breast carcinoma cell-line MCF7, treated with 1uM RITA for 24h

hyb_protocol: Labeled cRNA was fragmented in  fragmentation buffer (5× buffer: 200 mM Tris-acetate (pH 8.1)/500 mM KOAc/150 mM  MgOAc) and hybridized to the microarrays in 200μl of hybridization solution containing  10μg labeled target in 1× Mes buffer (0.1 M Mes/1.0 M NaCl/20 mM EDTA  0.01%/Tween20) and 0.1mg/ml herring sperm DNA, 0.5mg/ml BSA, 50 pM control  oligonucleotide B2 and 1x eukaryotic hybridization controls (bioB, bioC, bioD, cre).  Both control oligonucleotide B2 and eukaryotic hybridization controls were purchased  from Affymetrix.          Samples were then hybridized on Human Genome U133A 2.0 Arrays  (Affymetrix). Arrays were placed on a rotisserie and rotated at 60rpm for 16h at 45°C.  Following hybridization, the arrays were washed with 6× SSPE-T (0.9 M NaCl/60 mM  NaH2PO4/6 mM EDTA/0.01% Tween20) at 25°C on a fluidics station (Affymetrix) for 10  cycles of 2 mixes/cycle, and subsequently with 0.1M Mes/0,1 M NaCl/0.01 % Tween20  at 50°C for 4 cycles of 15 mixes/cycle. The arrays were then stained with a  streptavidin-phycoerythrin conjugate (Molecular Probes), followed by 10 washing cycles  of 4 mixes/cycle with 6x SSPE-T. To enhance the signals, the arrays were further  stained with Anti-streptavidin antibody solution for 10 min at 25°C followed by a 10 min  staining with a streptavidin-phycoerythrin conjugate. After 15 washing cycles of 4  mixes/cycle, the arrays were scanned using a confocal scanner (Affymetrix).

scan_protocol: The arrays were scanned using a confocal scanner (Affymetrix)

data_processing: The image data were analyzed by GCOS 1.4 (GeneChip Operating Software, Affymetrix).

source_name: MCF7 cells treated with 1uM RITA for 24h

label_protocol: Starting from 2μg of total RNA of 46 from the 54 samples available, cDNA was  synthesized with One-Cycle cDNA Synthesis kit from Affymetrix, by following the  Affymetrix Expression Analysis Technical Manual protocol.           cRNA was synthesized from cDNA by following the IVT Labeling kit  (Affymetrix). cRNA was purified with the GeneChip Sample Cleanup Module from  Affymetrix and eluted in 22μl of RNase-free water

growth_protocol: MCF7 cells were grown in IMDM medium

extract_protocol: Total RNA was extracted using RNEasy kit from QIAGEN.

treatment_protocol: Exponentially growing cell cultures were either left untreated or treate with 1uM RITA.

tag: 1uM RITA, 24h


title: 0mg/kg/day PFOS, lung rep5

description: Fetal lung gene expression data from full term pups exposed to PFOS throughout gestation.


title: 0mg/kg/day PFOS, liver rep5


title: MCF7 1uM 8h

description: Breast carcinoma cell-line MCF7, treated with 1uM RITA for 8h

source_name: MCF7 cells treated with 1uM RITA for 8h

tag: 1uM RITA, 8h


title: PBLs_pair 227565_ICF

description: gene expression data from PBLs, pair 227565, ICF, male

source_name: PBLs, pair 227565, ICF


title: PBLs_pair 232496_unaffected

description: gene expression data from PBLs, pair 232496, unaffected, female

source_name: PBLs, pair 232496, unaffected


title: PBLs_pair 227565_unaffected

description: gene expression data from PBLs, pair 227565, unaffected, male

source_name: PBLs, pair 227565, unaffected


title: MCF7 1uM 16h

description: Breast carcinoma cell-line MCF7, treated with 1uM RITA for 16h

source_name: MCF7 cells treated with 1uM RITA for 16h

tag: 1uM RITA, 16h


title: 0mg/kg/day PFOS, liver rep4


title: CHM008Sty

source_name: complete hydatidiform mole


title: 0mg/kg/day PFOS, lung rep4


title: PBLs_pair 235495_ICF

description: gene expression data from PBLs, pair 235495, ICF, female

source_name: PBLs, pair 235495, ICF


title: PBLs_pair 232496_CFS

description: gene expression data from PBLs, pair 232496, CFS, female

source_name: PBLs, pair 232496, CFS


title: Mat-Lylu cell line 1

city: Valhalla

first: Ismael

last: Reyes

address: Microbiology department BSB room 311

institute: New York Medical College

description: rat highly-metastatic prostate cancer cell line

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: dChip v 1.3 was used for normalization, model-based gene expression estimatation and outlier detection ; Affymetrix Microarray Suite version 5.0 was used to calculate the present call of each transcript

organism: Rattus norvegicus

source_name: Dunning R3327 rat prostatic tumor sublines

label_protocol: Approximately 10 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: standard Affymetrix procedures

tag: Rat metastatic prostate cancer cell line sample


title: CHM011Sty


title: G cell line 0

description: rat non-metastatic prostate cancer cell line

tag: Rat non-metastatic prostate cancer cell line sample


title: PBLs_pair 235495_unaffected

description: gene expression data from PBLs, pair 235495, unaffected, female

source_name: PBLs, pair 235495, unaffected


title: CHM005Sty


title: MCF7 1uM untreated

description: Breast carcinoma cell-line MCF7.

source_name: untreated MCF7 cells

tag: untreated


title: G cell line 1


title: CHM009Sty


title: Mat-Lylu cell line 0


title: MCF7 1uM 2h

description: Breast carcinoma cell-line MCF7, treated with 1uM RITA for 2h

source_name: MCF7 cells treated with 1uM RITA for 2h

tag: 1uM RITA, 2h


title: 0mg/kg/day PFOS, liver rep2

source_name: Fetal liver, CD-1 background


title: 0mg/kg/day PFOS, liver rep3


title: 0mg/kg/day PFOS, lung rep3

source_name: Fetal lung, CD-1 background


title: PBLs_pair 228340_CFS

description: gene expression data from PBLs, pair 228340, CFS, female

source_name: PBLs, pair 228340, CFS

tag: twin pair

tag: sex


title: PBLs_pair 220263_CFS

description: gene expression data from PBLs, pair 220263, CFS, female

source_name: PBLs, pair 220263, CFS

tag: diagnonsis


title: 0mg/kg/day PFOS, liver rep1

description: Fetal liver gene expression data from full term pups exposed to PFOS throughout gestation.


title: 0mg/kg/day PFOS, lung rep2


title: PBLs_pair 220263_unaffected

description: gene expression data from PBLs, pair 220263, unaffected, female

source_name: PBLs, pair 220263, unaffected


title: CHM007Sty


title: PBLs_pair 230813_unaffected

description: gene expression data from PBLs, pair 230813, unaffected, female

source_name: PBLs, pair 230813, unaffected


title: PBLs_pair 228340_unaffected

description: gene expression data from PBLs, pair 228340, unaffected, female

source_name: PBLs, pair 228340, unaffected


title: 0mg/kg/day PFOS, lung rep1

description: Fetal lung gene expression data from full term pups exposed to PFOS throughout gestation.


title: CHM003Sty


title: CHM006Sty


title: SH-SY5Y_5ppm_48h-R3

status: Public on May 11 2009

city: Augusta

first: Pachiappan

last: Arjunan

state: Georgia

address: 1120 15th ST, Laney walker Blvd,

department: Anatomy, Unit on Retinal Vascular Neurobiology, BMB

institute: NUS, NIH, GRU

description: Total RNA was isolated from sarin (5ppm)treated  (n = 6 flasks, 48h) neuronal (SH-SY5Y) cell lines using RNeasy® mini kit. The preparation and processing of labeled, fragmented cRNA for hybridization has been performed according to the manufacturer’s protocols (Affymetrix, Santa Clara, CA). Replicate-3.

data_processing: Data generated from MAS5.0, all raw data scaled to 800

label: SAPE

source_name: Human Brain neuronal (SH-SY5Y) cell lines

tag: Human brain neuronal (SH-SY5Y) cell lines treated with 5ppm of sarin (GB) and incubated for 48 h (Sarin treated, 48h-Replicate-3).


title: CHM001Sty


title: CHM002Sty


title: SH-SY5Y_5ppm_24h-R1

description: Total RNA was isolated from Sarin (5ppm) treated  (n = 6 flasks, 24h) neuronal (SH-SY5Y) cell lines using RNeasy® mini kit. The preparation and processing of labeled, fragmented cRNA for hybridization has been performed according to the manufacturer’s protocols (Affymetrix, Santa Clara, CA). Replicate-1.

tag: Human brain neuronal (SH-SY5Y) cell lines treated with 5ppm of sarin (GB) and incubated for 24 h (Sarin treated, 24h-Replicate-1).


title: SH-SY5Y_Ctrl_48h-R3

description: Total RNA was isolated from untreated  (n = 6 flasks, 48h) neuronal (SH-SY5Y) cell lines using RNeasy® mini kit. The preparation and processing of labeled, fragmented cRNA for hybridization has been performed according to the manufacturer’s protocols (Affymetrix, Santa Clara, CA). Replicate-3.

tag: Human brain neuronal (SH-SY5Y) cell lines and incubated for 48 h (Control, 48h-Replicate-3).


title: SH-SY5Y_5ppm_3h-R2

description: Total RNA was isolated from sarin treated  (n = 6 flasks, 3h) neuronal (SH-SY5Y) cells using RNeasy® mini kit. The preparation and processing of labeled, fragmented cRNA for hybridization has been performed according to the manufacturer’s protocols (Affymetrix, Santa Clara, CA). Replicate-2.

tag: Human brain neuronal (SH-SY5Y) cell lines treated with 5ppm of sarin (GB) and incubated for 3 h (Sarin treated, 3h-Replicate-2).


title: SH-SY5Y_Ctrl_24h-R3

description: Total RNA was isolated from untreated  (n = 6 flasks, 24h) neuronal (SH-SY5Y) cell lines using RNeasy® mini kit. The preparation and processing of labeled, fragmented cRNA for hybridization has been performed according to the manufacturer’s protocols (Affymetrix, Santa Clara, CA). Replicate-3.

tag: Human brain neuronal (SH-SY5Y) control cell lines and incubated for 24 h (Control, 24h-Replicate-3).


title: SH-SY5Y_Ctrl_48h-R2

description: Total RNA was isolated from untreated  (n = 6 flasks, 48h) neuronal (SH-SY5Y) cell lines using RNeasy® mini kit. The preparation and processing of labeled, fragmented cRNA for hybridization has been performed according to the manufacturer’s protocols (Affymetrix, Santa Clara, CA). Replicate-2.

tag: Human brain neuronal (SH-SY5Y) cell lines and incubated for 48 h (Control, 48h-Replicate-2).


title: SH-SY5Y_Ctrl_3h-R3

description: Total RNA was isolated from untreated control (n = 6 flasks) cells using RNeasy® mini kit. The preparation and processing of labeled, fragmented cRNA for hybridization has been performed according to the manufacturer’s protocols (Affymetrix, Santa Clara, CA). Replicate-3.

tag: Human brain neuronal (SH-SY5Y) cell lines (Control, Replicate-3)


title: PBMC Group B, biological rep 6 (HumanRef-8)

city: Berkeley

first: Cliona

last: McHale

state: CA

address: 384 Li Ka Shing Center

department: School of Public Health

institute: University of California Berkeley

hyb_protocol: Following fragmentation, 850ng of cRNA were hybridized for 16 hr at 55C on Illumina Sentrix HumanRef-8 chips. Hybridization, washing and detection were performed using Illumina's Gene Expression System Buffer Kit according to the manufacturer's instructions.

scan_protocol: Scanning was performed using a BeadArray Reader and BeadScan software (Illumina)

data_processing: Data were normalized using quantile normalization from the Bioconductor Affymetrix package.

source_name: PBMC Group B

label_protocol: cDNA was generated from total RNA (200ng) and used as a template for the in vitro transcription of biotin-labeled cRNA using the Illumina® RNA Amplification kit (Ambion, Austin, TX) according to the manufacturer’s protocol.

extract_protocol: Peripheral blood was collected from each subject at the beginning of the workday around 0900 hr and processed within 6 hr of collection. PBMC were isolated by Ficoll-Paque and lysed in RLT buffer (Qiagen). Lysates were frozen at -80°C and later thawed and extracted using Qiagen's RNeasy mini kit according to the manufacturer's instructions.

tag: Male


title: PBMC Group B, biological rep 1 (HumanRef-8)


title: SH-SY5Y_Ctrl_24h-R1

description: Total RNA was isolated from untreated  (n = 6 flasks, 24h) neuronal (SH-SY5Y) cells using RNeasy® mini kit. The preparation and processing of labeled, fragmented cRNA for hybridization has been performed according to the manufacturer’s protocols (Affymetrix, Santa Clara, CA). Replicate-1.

tag: Human brain neuronal (SH-SY5Y) control cell lines and incubated for 24 h (Control, 24h-Replicate-1).


title: PBMC Group B, biological rep 5 (HumanRef-8)


title: PBMC Group B, biological rep 3 (HumanRef-8)


title: SH-SY5Y_Ctrl_48h-R1

description: Total RNA was isolated from untreated  (n = 6 flasks, 48h) neuronal (SH-SY5Y) cell lines using RNeasy® mini kit. The preparation and processing of labeled, fragmented cRNA for hybridization has been performed according to the manufacturer’s protocols (Affymetrix, Santa Clara, CA). Replicate-1.

tag: Human brain neuronal (SH-SY5Y) cell lines and incubated for 48 h (Control, 48h-Replicate-1).


title: SH-SY5Y_5ppm_24h-R2

description: Total RNA was isolated from Sarin (5ppm) treated  (n = 6 flasks, 24h) neuronal (SH-SY5Y) cell lines using RNeasy® mini kit. The preparation and processing of labeled, fragmented cRNA for hybridization has been performed according to the manufacturer’s protocols (Affymetrix, Santa Clara, CA). Replicate-2.

tag: Human brain neuronal (SH-SY5Y) cell lines treated with 5ppm of sarin (GB) and incubated for 24 h (Sarin treated, 24h-Replicate-2).


title: PBMC Group B, biological rep 8 (HumanRef-8)

tag: Female


title: PBMC Group A, biological rep 7 (HumanRef-8)

source_name: PBMC Group A


title: PBMC Group A, biological rep 8 (HumanRef-8)


title: SH-SY5Y_Ctrl_3h-R2

description: Total RNA was isolated from untreated control (n = 6 flasks) cells using RNeasy® mini kit. The preparation and processing of labeled, fragmented cRNA for hybridization has been performed according to the manufacturer’s protocols (Affymetrix, Santa Clara, CA). Replicate-2.

tag: Human brain neuronal (SH-SY5Y) cell lines (Control, Replicate-2)


title: SH-SY5Y_5ppm_3h-R1

description: Total RNA was isolated from sarin treated  (n = 6 flasks, 3h) neuronal (SH-SY5Y) cells using RNeasy® mini kit. The preparation and processing of labeled, fragmented cRNA for hybridization has been performed according to the manufacturer’s protocols (Affymetrix, Santa Clara, CA). Replicate-1.

tag: Human brain neuronal (SH-SY5Y) cell lines treated with 5ppm of sarin (GB) and incubated for 3 h (Sarin treated, 3h-Replicate-1).


title: SH-SY5Y_5ppm_48h-R1

description: Total RNA was isolated from sarin (5ppm)treated  (n = 6 flasks, 48h) neuronal (SH-SY5Y) cell lines using RNeasy® mini kit. The preparation and processing of labeled, fragmented cRNA for hybridization has been performed according to the manufacturer’s protocols (Affymetrix, Santa Clara, CA). Replicate-1.

tag: Human brain neuronal (SH-SY5Y) cell lines treated with 5ppm of sarin (GB) and incubated for 48 h (Sarin treated, 48h-Replicate-1).


title: SH-SY5Y_5ppm_3h-R3

description: Total RNA was isolated from sarin treated  (n = 6 flasks, 3h) neuronal (SH-SY5Y) cells using RNeasy® mini kit. The preparation and processing of labeled, fragmented cRNA for hybridization has been performed according to the manufacturer’s protocols (Affymetrix, Santa Clara, CA). Replicate-3.

tag: Human brain neuronal (SH-SY5Y) cell lines treated with 5ppm of sarin (GB) and incubated for 3 h (Sarin treated, 3h-Replicate-3).


title: SH-SY5Y_5ppm_24h-R3

description: Total RNA was isolated from Sarin (5ppm) treated  (n = 6 flasks, 24h) neuronal (SH-SY5Y) cell lines using RNeasy® mini kit. The preparation and processing of labeled, fragmented cRNA for hybridization has been performed according to the manufacturer’s protocols (Affymetrix, Santa Clara, CA). Replicate-3.

tag: Human brain neuronal (SH-SY5Y) cell lines treated with 5ppm of sarin (GB) and incubated for 24 h (Sarin treated, 24h-Replicate-3).


title: PBMC Group B, biological rep 4 (HumanRef-8)


title: PBMC Group B, biological rep 7 (HumanRef-8)


title: PBMC Group B, biological rep 2 (HumanRef-8)


title: SH-SY5Y_5ppm_48h-R2

description: Total RNA was isolated from sarin (5ppm)treated  (n = 6 flasks, 48h) neuronal (SH-SY5Y) cell lines using RNeasy® mini kit. The preparation and processing of labeled, fragmented cRNA for hybridization has been performed according to the manufacturer’s protocols (Affymetrix, Santa Clara, CA). Replicate-2.

tag: Human brain neuronal (SH-SY5Y) cell lines treated with 5ppm of sarin (GB) and incubated for 48 h (Sarin treated, 48h-Replicate-2).


title: SH-SY5Y_Ctrl_24h-R2

description: Total RNA was isolated from untreated  (n = 6 flasks, 24h) neuronal (SH-SY5Y) cell lines using RNeasy® mini kit. The preparation and processing of labeled, fragmented cRNA for hybridization has been performed according to the manufacturer’s protocols (Affymetrix, Santa Clara, CA). Replicate-2.

tag: Human brain neuronal (SH-SY5Y) control cell lines and incubated for 24 h (Control, 24h-Replicate-2).


title: PBMC Group A, biological rep 5 (HumanRef-8)


title: PBMC Group A, biological rep 6 (HumanRef-8)


title: PBMC Group A, biological rep 3 (HumanRef-8)


title: PBMC Group A, biological rep 4 (HumanRef-8)


title: PBMC Group A, biological rep 1 (HumanRef-8)


title: ChIP CTCF Treg replicate 1

city: Regensburg

first: Christian

last: Schmidl

address: Franz-Josef-Strauss-Allee 11

country: Germany

institute: Rengensburg Center for Interventional Immunology

hyb_protocol: Samples were hybridized using a stringent protocol.The differentially labeled input and ChIP sample were combined and supplemented with 25 µg human Cot-1 DNA (Invitrogen), 26 µl of Agilent blocking agent (10-fold) (Agilent) and 130 µl Agilent hybridization buffer (2-fold) as supplied in the Agilent oligo aCGH Hybridization kit. The samples were heated to 95° for 3 min, mixed and subsequently incubated at 37°C for 30 min. Hybridization was then carried out 65°C for 40 h using an SureHyb chamber and an Agilent hybridization oven. Slides were washed in Wash I (6xSSPE, 0.005% N-lauroylsarcosine) at room temperature for 5 min and in Wash II (0.06xSSPE) for an additional 5 min. Afterwards slides were dried using acetonitrile within an ozone free facility.

scan_protocol: Scanned on an Agilent scanner at 5 µm resolution.Images were quantified using Agilent Feature Extraction Software (version 9.5.1).

data_processing: Linear normalized, background subtracted VALUE data obtained from log10 of processed Red signal/processed Green signal. Agilent software was used. Processed signal intensities were further normalized using GC-dependent regression and imported into Microsoft Office Excel 2007 for further analysis. Probes with abnormal hybridization behavior (extremely low (2507 probes) or high (5149 probes) signal intensities in both channels) were excluded.

label: Alexa Fluor 555–aha–dCTP

source_name: CD4+CD25+CD45RA+ Treg

label_protocol: ChIP samples were amplified with ligation mediated PCR (LM-PCR) prior to labeling: ChIP and input DNA were blunted and phosphorylated for 30 minutes at 20 °C in 50 µl reactions containing 10x T4 DNA ligase buffer, 2 µl dNTP mix (10 mM each), 3 U T4 DNA polymerase, 10 U T4 polynucleotide kinase and 1 U Klenow DNA polymerase. Purification using the Qiaquick PCR purification kit (Qiagen) was followed by the addition of Adenine to 3’-ends using Klenow fragment (3’ to 5’ exo minus), and dATP (1 mM) for 30 minutes at 37 °C. After clean-up using the MinElute kit (Qiagen), DNA fragments were ligated to linker DNA (60 µM pre-annealed JW102s 5'-GCG GTG ACC CGG GAG ATC TGA ATT CT-3' and JW103 5'-GAA TTC AGA TC-3') with 4 µl DNA Quick-Ligase (NEB) in a 30 µl reaction for 15 minutes at RT. Samples were cleaned-up (Qiaquick PCR purification kit (Qiagen)) and amplified using Phusion Polymerase and JW102s oligonucleotide for 15 cycles. The product of the first amplification was diluted 1/20 with ddH2O and 5 µl of the dilution were used for a second round of amplification (15 cycles) using Phusion Polymerase HOT START and JW102s oligonucleotide. The amplified ChIP and input material was purified using Qiaquick PCR purification kit (Qiagen). Then 1µg each of the samples were fluorescently labeled for microarray hybridization by direct labeling with Alexa Fluor 555–aha–dCTP and Alexa Fluor 647–aha–dCTP using the BioPrime Plus Array CGH Genomic Labeling System (Invitrogen; Version A, 12 February 2007) according to the manufacturer's intruction.

growth_protocol: Treg and Tconv cell isolation and expansion culture was performed as previously described by Hoffmann et al. 2004 (Blood. Aug 1;104(3):895-903). Cell-culture was performed according to Hoffmann et al. 2006 (Blood. Dec 15;108(13):4260-7).

extract_protocol: Genomic DNA was prepared using the Qiagen Blood & Cell Culture DNA Kit or the Qiagen DNeasy Blood & Tissue Kit according to the manufacturer's instruction.

treatment_protocol: Treg and Tconv cell FACS sorting and expansion culture was performed as previously described by Hoffmann et al. 2004 (Blood. Aug 1;104(3):895-903). Cell-culture was performed according to Hoffmann et al. 2006 (Blood. Dec 15;108(13):4260-7).

tag: Antibody is a gift from V. Lobanenkow

tag: gender

tag: CD4+CD25+CD45RA+ regulatory T-cells

tag: expansion cultures

label: Alexa Fluor 647–aha–dCTP

source_name: Input (4% volumen of Lysate)


title: ChIP CTCF Treg replicate 2


title: Ovarian tumor sample 330

status: Public on May 20 2009

city: Groningen

first: Rudolf

middle: Stephan Nicolaas

last: Fehrmann

state: Groningen

department: Gynecologic Oncology

institute: University Medical Center Groningen

description: Channel 2 in raw data file ; Characteristics: STATUS: 0 = end of follow-up or death unrelated to ovarian cancer ;  1 = death due to ovarian cancer FUMND: Months from primary surgery SAMPLE NR: Unique RNA reference number

hyb_protocol: Protocol is available at http://microarrays.nki.nl/download/protocols/Hybridization_oligo_array_ULS_labeling_of_aRNA_2005.pdf

scan_protocol: Arrays were scanned with the Affymetrix GMS428 scanner (Affymetrix, Santa Clara, CA) and expression values were calculated by BlueFuse software (BlueGnome, Cambridge, UK).

data_processing: raw data

source_name: Advanced stage serous ovarian cancer

label_protocol: All cRNA samples (1.5 µg) were labeled with ULS-Cy5 and ULS-Cy3 label (BIOKÉ, Leiden, the Netherlands).

growth_protocol: All tumor samples were flash frozen in liquid nitrogen and stored at -80 °C.

extract_protocol: Total RNA from tumor samples was pelleted through cesium chloride density gradient ultracentrifugation (Roche, Almere, the Netherlands). After total RNA samples had been given DNAse treatment (Megascript T7 kit, Ambion, Huntingdon, UK), they were checked for residual DNA using a dinucleotide primer set D11S875 specific for genomic DNA. mRNA was linearly amplified by in vitro transcription using T7 RNA polymerase (Megascript T7 kit, Ambion, Huntingdon, UK) [13]. Quality/integrity of total and amplified mRNA (cRNA) was checked by spectrophotometer analysis, UV 260/280 ratio > 1.8, and/or agarose gel electrophoresis.

treatment_protocol: All tumor samples were obtained at primary surgery prior to chemotherapy.

tag: assigned unique patient id

tag: status

tag: fumnd

tag: age

tag: sample nr


title: ChIP H3K4 dimethyl Tconv replicate 1

source_name: CD4+CD25- Tconv

tag: Antibody from Upstate

tag: CD4+CD25- conventional T-cells


title: PBMC Group A, biological rep 2 (HumanRef-8)

tag: Female


title: ChIP CTCF Tconv replicate 2


title: SH-SY5Y_Ctrl_3h-R1

description: Total RNA was isolated from untreated control (n = 6 flasks) cells using RNeasy® mini kit. The preparation and processing of labeled, fragmented cRNA for hybridization has been performed according to the manufacturer’s protocols (Affymetrix, Santa Clara, CA).Replicate-1

tag: Human brain neuronal (SH-SY5Y) cell lines (Control, Replicate1)


title: ChIP H3K4 trimethyl Treg replicate 3